86 research outputs found
Statistical Mechanical Approach to Human Language
We use the formulation of equilibrium statistical mechanics in order to study
some important characteristics of language. Using a simple expression for the
Hamiltonian of a language system, which is directly implied by the Zipf law, we
are able to explain several characteristic features of human language that seem
completely unrelated, such as the universality of the Zipf exponent, the
vocabulary size of children, the reduced communication abilities of people
suffering from schizophrenia, etc. While several explanations are necessarily
only qualitative at this stage, we have, nevertheless, been able to derive a
formula for the vocabulary size of children as a function of age, which agrees
rather well with experimental data.Comment: 20 pages,4 figures, Accepted in Physica
Rigid rotators and diatomic molecules via Tsallis statistics
We obtain an analytic expression for the specific heat of a system of N rigid
rotators exactly in the high temperature limit, and via a pertubative approach
in the low temperature limit. We then evaluate the specific heat of a diatomic
gas with both translational and rotational degrees of freedom, and conclude
that there is a mixing between the translational and rotational degrees of
freedom in nonextensive statistics.Comment: 12 page
APE in the wild: automated exploration of proteomics workflows in the bio.tools registry
The bio.tools registry is a main catalogue of computational tools in the life sciences. More than 17 000 tools have been registered by the international bioinformatics community. The bio.tools metadata schema includes semantic annotations of tool functions, that is, formal descriptions of tools' data types, formats, and operations with terms from the EDAM bioinformatics ontology. Such annotations enable the automated composition of tools into multistep pipelines or workflows. In this Technical Note, we revisit a previous case study on the automated composition of proteomics workflows. We use the same four workflow scenarios but instead of using a small set of tools with carefully handcrafted annotations, we explore workflows directly on bio.tools. We use the Automated Pipeline Explorer (APE), a reimplementation and extension of the workflow composition method previously used. Moving "into the wild" opens up an unprecedented wealth of tools and a huge number of alternative workflows. Automated composition tools can be used to explore this space of possibilities systematically. Inevitably, the mixed quality of semantic annotations in bio.tools leads to unintended or erroneous tool combinations. However, our results also show that additional control mechanisms (tool filters, configuration options, and workflow constraints) can effectively guide the exploration toward smaller sets of more meaningful workflows.Proteomic
Language Time Series Analysis
We use the Detrended Fluctuation Analysis (DFA) and the Grassberger-Proccacia
analysis (GP) methods in order to study language characteristics. Despite that
we construct our signals using only word lengths or word frequencies, excluding
in this way huge amount of information from language, the application of
Grassberger- Proccacia (GP) analysis indicates that linguistic signals may be
considered as the manifestation of a complex system of high dimensionality,
different from random signals or systems of low dimensionality such as the
earth climate. The DFA method is additionally able to distinguish a natural
language signal from a computer code signal. This last result may be useful in
the field of cryptography.Comment: 21 pages, 5 figures, accepted in Physica
Computational modeling to elucidate molecular mechanisms of epigenetic memory
How do mammalian cells that share the same genome exist in notably distinct
phenotypes, exhibiting differences in morphology, gene expression patterns, and
epigenetic chromatin statuses? Furthermore how do cells of different phenotypes
differentiate reproducibly from a single fertilized egg? These are fundamental
problems in developmental biology. Epigenetic histone modifications play an
important role in the maintenance of different cell phenotypes. The exact
molecular mechanism for inheritance of the modification patterns over cell
generations remains elusive. The complexity comes partly from the number of
molecular species and the broad time scales involved. In recent years
mathematical modeling has made significant contributions on elucidating the
molecular mechanisms of DNA methylation and histone covalent modification
inheritance. We will pedagogically introduce the typical procedure and some
technical details of performing a mathematical modeling study, and discuss
future developments.Comment: 36 pages, 4 figures, 2 tables, book chapte
Black hole thermodynamical entropy
As early as 1902, Gibbs pointed out that systems whose partition function
diverges, e.g. gravitation, lie outside the validity of the Boltzmann-Gibbs
(BG) theory. Consistently, since the pioneering Bekenstein-Hawking results,
physically meaningful evidence (e.g., the holographic principle) has
accumulated that the BG entropy of a black hole is
proportional to its area ( being a characteristic linear length), and
not to its volume . Similarly it exists the \emph{area law}, so named
because, for a wide class of strongly quantum-entangled -dimensional
systems, is proportional to if , and to if
, instead of being proportional to (). These results
violate the extensivity of the thermodynamical entropy of a -dimensional
system. This thermodynamical inconsistency disappears if we realize that the
thermodynamical entropy of such nonstandard systems is \emph{not} to be
identified with the BG {\it additive} entropy but with appropriately
generalized {\it nonadditive} entropies. Indeed, the celebrated usefulness of
the BG entropy is founded on hypothesis such as relatively weak probabilistic
correlations (and their connections to ergodicity, which by no means can be
assumed as a general rule of nature). Here we introduce a generalized entropy
which, for the Schwarzschild black hole and the area law, can solve the
thermodynamic puzzle.Comment: 7 pages, 2 figures. Accepted for publication in EPJ
Multi-omics Analyses of Starvation Responses Reveal a Central Role for Lipoprotein Metabolism in Acute Starvation Survival in <i>C. elegans</i>
Starvationcauses comprehensivemetabolicchanges, which are still not fully understood. Here, we used quantitative proteomics and RNA sequencing to examine the temporal starvation responses in wildtype Caenorhabditis elegans and animals lacking the transcription factor HLH-30. Our findings show that starvation alters the abundance of hundreds of proteins and mRNAs in a temporal manner, many of which are involved in central metabolic pathways, including lipoprotein metabolism. We demonstrate that premature death of hlh-30 animals under starvation can be prevented by knockdown of either vit-1 or vit-5, encoding two different lipoproteins. We further showthat the size and number of intestinal lipid droplets under starvation are altered in hlh-30 animals, which can be rescued by knockdown of vit-1. Taken together, this indicates that survival of hlh-30 animals under starvation is closely linked to regulation of intestinal lipid stores. We provide the most detailed poly-omic analysis of starvation responses to date, which serves as a resource for further mechanistic studies of starvation
- âŠ